Despite the considerable success of molecular biology to understand diseases such as cancer, many questions remain unanswered. One area that has remained particularly unexplored so far is related to the fact that since the majority of gene products mediate their function together with other gene products, biological processes should be considered as complex networks of interconnected components. It is increasingly apparent that such complex networks have properties of their own. Thus, to understand any normal biological process of interest, or any disease mechanism such as cancer, one should consider a "systems approach" that allows, in addition to precise studies of single proteins or RNAs one at-a-time, more global analyses of the properties and functions of the molecular networks in which they function (1, 2). Since many gene products mediate their function, and are regulated, through protein-protein interactions, we have proposed and demonstrated using the nematode C. elegans as a model system that one way to accelerate the discovery of candidate cancer genes and begin to assign their products to potential functional networks is to comprehensively map such protein-protein interactions to generate so-called "interactome" maps. We have also learned how to integrate such interactome maps with other functional genomic and/or proteomic maps. Such integration provides first-generation wiring diagrams of functional networks that include the worm orthologs of important human cancer genes. Here, we describe i) further applications of our newly developed technologies to improve the quality and reliability of our interactome maps and ii) the transfer of these technologies to the mouse proteome, a model more closely related to human cancer than C. elegans. Our specific aims are to: i) improve the quality and reliability of interactome maps by adapting a Multisite Gateway technology in order to systematically map discrete interaction domains, ii) improve the quality and reliability of interactome maps by using the versatility of the Gateway technology to exogenously express large numbers of proteins and thereby confirming protein-protein interactions, and iii) apply these technologies to the mapping of the mouse interactome that is more likely to be relevant to human cancer.